Methicillin resistant Staphylococcus aureus is an economically important disease causing bacteria for ruminants (Cattle buffalo, sheep and goat). The study examined the milk (350) and nasal swab samples (375) for detection of MRSA. The main goal of this study is genotyping of MRSA isolates are to assign phylogenetic links, clonal relationships, and clonal relatedness to strains between different species of ruminants. Methicillin resistant Staphylococcus aureus was identified based on growth in mannitol salt agar mixed oxacillin-resistant selective supplement, Gram’s staining, catalase tests and polymerase chain reaction (PCR) detection of mecA gene. The disc diffusion test was used to determine the antibiotic resistant against methicillin disk and mecA, spa and whole gene sequence typing for genotyping of isolates for preparation of phylogeny tree. Out of 625 samples 171 samples were positive growth in mannitol salt agar mixed oxacillin-resistant selective supplement. These isolates were further characterized by grams staining and catalase test. Out of 171 methicillin resistance S. aureus isolates recovered from cattle, buffalo, sheep and goat during this study, mecA gene was amplified in 137 (80.11 %) isolates with an amplicon size of 533 kb. On the basis of spa gene data, On the basis of spa gene data, the sequences were analyzed and a phylogenetic tree was drawn in Tree-Base in which SPA7 (MRSA isolate from nasal swab sample of goat) was found to be more distantly related to other isolates. Nasal swab and milk from ruminants were positive for MRSA. All mecA positive MRSA isolates were also resistant for methicillin antibiotic disc. Moreover the genotypes of some MRSA isolates were found different in ruminants.